After a slow first half, the Super Eagles took the lead from the spot when William Troost-Ekong fired home from the spot after Victor Osimhen was brought down.
The favourites thought they had doubled the lead in the dying moments of regular time when Osimhen slammed home but a VAR check not only ruled out the goal but awarded South Africa a penalty after Alhassan Yusuf fouled Percy Tau inside the box.
Teboho Mokoena levelled from the spot before Khuliso Mudau spurned a golden opportunity to win the game for Bafana Bafana in the dying moments.
Grant Kekana saw red for South Africa in an otherwise quiet extra-time before Nigeria emerged victorious from the penalty shootout.
Nigeria goalkeeper Stanley Nwabali saved two penalties in the shootout to guide his side to a 4-2 victory over South Africa following a 1-1 draw on Wednesday and earn a place in the Africa Cup of Nations final.
Nigeria had lost five of their previous six semi-finals at the continental finals but survived some nervous moments to book a place in Sunday’s decider against either hosts Ivory Coast or the Democratic Republic of Congo, who meet later on Wednesday.
William Troost-Ekong put Nigeria into the lead from the penalty spot midway through the second half, before South Africa earned a spot-kick of their own in the final minute of the 90 and it was converted by Teboho Mokoena.
South Africa lost defender Grant Kekana to a red card in extra time as Nigeria put them under constant pressure, and then lost their nerve too in the shootout as Nwabali saved from Mokoena and Evidence Makgopa.
What we know
- Nigeria book place in Sunday’s final after dramatic penalty shootout win
- Game heads to penalties after 1-1 draw after extra-time
- ‘115 RED CARD! Kekana sees red after VAR check (NGA 1-1 RSA)
- ‘90+6 CHANCE! Mudau spurns golden late opportunity (NGA 1-1 RSA)
- ‘90 GOAL! Mokoena equalises after VAR drama (NGA 1-1 RSA)
- ‘67 GOAL! Troost-Ekong converts from spot (NGA 1-0 RSA)